Annovar result GT field

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4.8 years ago

vaish01kv • 0

I annotated my tumor-normal sample using ANNOVAR. The genotype field (GT) was 0/0 for normal and 0/1 for tumor. Can someone please explain, why do i get 0/0 for normal sample? I'm a beginner & still couldn't understand the concept of GT in VCF file. TIA.

genotype GT annovar • 1.0k views

ADD COMMENT • link 4.8 years ago by vaish01kv • 0

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why do i get 0/0 for normal sample?

what did you expect for a normal sample ?

ADD REPLY • link 4.8 years ago by Pierre Lindenbaum 161k

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Thanks for your reply. Could you please clarify the difference between genotypes 0/1, 0/2, 0/1/2?

ADD REPLY • link 4.8 years ago by vaish01kv • 0

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Genotype representation with 0, 1, 2 - what do they mean?

ADD REPLY • link 4.8 years ago by Pierre Lindenbaum 161k

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I think you have multi variants at the some position , 0 is wild type if i remenber corretly, 1 the first variant possible etc

ADD REPLY • link 4.8 years ago by Titus ▴ 910

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Yes, how to infer from this data?

ADD REPLY • link 4.8 years ago by vaish01kv • 0

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You have not shown any data. To avoid confusion, please paste some examples of your data.

ADD REPLY • link 4.8 years ago by Kevin Blighe 87k

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